Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1861
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10632
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Found at i:1100 original size:16 final size:16
Alignment explanation
Indices: 1081--1111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1071 CTTCTTCACT
1081 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
1097 TACTTACTTACTTAA
1 TACTCACTTACTTAA
1112 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:1117 original size:20 final size:20
Alignment explanation
Indices: 1078--1117 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1068 AAACTTCTTC
* *
1078 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
1098 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
1118 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:1493 original size:55 final size:53
Alignment explanation
Indices: 1303--1557 Score: 236
Period size: 55 Copynumber: 4.8 Consensus size: 53
1293 ACACGGGTAC
* * * * *
1303 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* *
1352 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
* * *
1405 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA
* ***
1460 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* * * *
1513 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
1558 AAACCCTAAT
Statistics
Matches: 173, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
49 38 0.22
50 1 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 71 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
Found at i:1494 original size:108 final size:110
Alignment explanation
Indices: 1350--1547 Score: 321
Period size: 108 Copynumber: 1.8 Consensus size: 110
1340 ATCCTTTTGA
* *
1350 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
1413 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
1458 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
1523 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
1548 CGGTATCCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.60
109 7 0.09
110 25 0.30
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:7547 original size:17 final size:18
Alignment explanation
Indices: 7518--7552 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
7508 ACTAATATTC
7518 CGAGAACCGACTAAACCT
1 CGAGAACCGACTAAACCT
7536 CGAGAA-CGACTAAACCT
1 CGAGAACCGACTAAACCT
7553 TTGCTCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.40, C:0.31, G:0.17, T:0.11
Consensus pattern (18 bp):
CGAGAACCGACTAAACCT
Found at i:8658 original size:16 final size:16
Alignment explanation
Indices: 8639--8669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8629 CTTCTTCACT
8639 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
8655 TACTTACTTACTTAA
1 TACTCACTTACTTAA
8670 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:8675 original size:20 final size:20
Alignment explanation
Indices: 8636--8675 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8626 AAACTTCTTC
* *
8636 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
8656 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
8676 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:9107 original size:55 final size:55
Alignment explanation
Indices: 8964--9107 Score: 168
Period size: 55 Copynumber: 2.6 Consensus size: 55
8954 CCTTATGAAC
* * *
8964 TCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAAT
1 TCCATGCCTTGGCATGGTCTTACATGGTATCC-TTGCCTTATAGAAACTTACCAAT
* * * * *
9019 GCCATGTCTTGACATGGTCTTACATGATTTCCTTGCC-T-TAGAAACCTTACCAATT
1 TCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAAA-CTTACCAA-T
9074 TCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 TCCATGCCTTGGCATGGTCTTACATGGTATCCTT
9108 AAACCCTAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
53 5 0.07
54 8 0.11
55 58 0.79
56 2 0.03
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (55 bp):
TCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATAGAAACTTACCAAT
Done.